MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities

MatrixDB (http://matrixdb.ibcp.fr) is a freely available database focused on interactions established by extracellular proteins and polysaccharides. It is an active member of the International Molecular Exchange (IMEx) consortium and has adopted the PSI-MI standards for annotating and exchanging interaction data, either at the MIMIx or IMEx level. MatrixDB content has been updated by curation and by importing extracellular interaction data from other IMEx databases. Other major changes include the creation of a new website and the development of a novel graphical navigator, iNavigator, to build and expand interaction networks. Filters may be applied to build sub-networks based on a list of biomolecules, a specified interaction detection method and/or an expression level by tissue, developmental stage, and health state (UniGene data). Any molecule of the network may be selected and its partners added to the network at any time. Networks may be exported under Cytoscape and tabular formats and as images, and may be saved for subsequent re-use.

[1]  Adam J. Smith,et al.  The Database of Interacting Proteins: 2004 update , 2004, Nucleic Acids Res..

[2]  L. Castagnoli,et al.  mentha: a resource for browsing integrated protein-interaction networks , 2013, Nature Methods.

[3]  Nicola J. Mulder,et al.  A web-based protein interaction network visualizer , 2013, BMC Bioinformatics.

[4]  Sandhya Rani,et al.  Human Protein Reference Database—2009 update , 2008, Nucleic Acids Res..

[5]  HeerJeffrey,et al.  D3 Data-Driven Documents , 2011 .

[6]  G. Hong,et al.  Nucleic Acids Research , 2015, Nucleic Acids Research.

[7]  Karin Breuer,et al.  InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation , 2012, Nucleic Acids Res..

[8]  Sylvie Ricard-Blum,et al.  MatrixDB, a database focused on extracellular protein–protein and protein–carbohydrate interactions , 2009, Bioinform..

[9]  E. Chautard,et al.  Interaction networks as a tool to investigate the mechanisms of aging , 2010, Biogerontology.

[10]  Sylvie Ricard-Blum,et al.  MatrixDB, the extracellular matrix interaction database , 2010, Nucleic Acids Res..

[11]  E. Chautard,et al.  Extended interaction network of procollagen C-proteinase enhancer-1 in the extracellular matrix. , 2014, The Biochemical journal.

[12]  Johannes Goll,et al.  Protein interaction data curation: the International Molecular Exchange (IMEx) consortium , 2012, Nature Methods.

[13]  Rafael C. Jimenez,et al.  The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases , 2013, Nucleic Acids Res..

[14]  Jeffrey Heer,et al.  SpanningAspectRatioBank Easing FunctionS ArrayIn ColorIn Date Interpolator MatrixInterpola NumObjecPointI Rectang ISchedu Parallel Pause Scheduler Sequen Transition Transitioner Transiti Tween Co DelimGraphMLCon IData JSONCon DataField DataSc Dat DataSource Data DataUtil DirtySprite LineS RectSprite , 2011 .

[15]  Steven A. Carr,et al.  The Matrisome: In Silico Definition and In Vivo Characterization by Proteomics of Normal and Tumor Extracellular Matrices , 2011, Molecular & Cellular Proteomics.

[16]  Jeffrey Heer,et al.  D³ Data-Driven Documents , 2011, IEEE Transactions on Visualization and Computer Graphics.

[17]  María Martín,et al.  Activities at the Universal Protein Resource (UniProt) , 2013, Nucleic Acids Res..

[18]  A. Sobczyńska-Tomaszewska,et al.  The COL7A1 mutation database , 2012, Human mutation.

[19]  Rafael C. Jimenez,et al.  The IntAct molecular interaction database in 2012 , 2011, Nucleic Acids Res..

[20]  Ioannis Xenarios,et al.  DIP: The Database of Interacting Proteins: 2001 update , 2001, Nucleic Acids Res..

[21]  Robert D. Finn,et al.  InterPro in 2011: new developments in the family and domain prediction database , 2011, Nucleic acids research.

[22]  COLdb, a database linking genetic data to molecular function in fibrillar collagens , 2009, Human mutation.

[23]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[24]  Livia Perfetto,et al.  MINT, the molecular interaction database: 2012 update , 2011, Nucleic Acids Res..

[25]  Christie S. Chang,et al.  The BioGRID interaction database: 2013 update , 2012, Nucleic Acids Res..

[26]  Peter Woollard,et al.  The minimum information required for reporting a molecular interaction experiment (MIMIx) , 2007, Nature Biotechnology.

[27]  J. Esko,et al.  Heparan sulfate proteoglycans. , 2011, Cold Spring Harbor perspectives in biology.

[28]  Lennart Martens,et al.  The Ontology Lookup Service: bigger and better , 2010, Nucleic Acids Res..

[29]  Wilson Savino,et al.  Laminin-database v.2.0: an update on laminins in health and neuromuscular disorders , 2013, Nucleic Acids Res..

[30]  A. Ori,et al.  A Systems Biology Approach for the Investigation of the Heparin/Heparan Sulfate Interactome* , 2011, The Journal of Biological Chemistry.

[31]  Andrew C. R. Martin.  Databases and ontologies Mapping PDB chains to UniProtKB entries , 2005 .

[32]  Maria Jesus Martin,et al.  BioJS: an open source JavaScript framework for biological data visualization , 2013, Bioinform..

[33]  S. Ricard-Blum,et al.  Matrix Metalloproteinase , SPARC : Secreted Protein Acidic and Rich in Cysteine , VEGF : Vascular Endothelial Growth Factor Keywords Matricryptins-Matrikines-Extracellular matrix-Bioactive fragments – Endostatin , 2014 .

[34]  E. Chautard,et al.  The First Draft of the Endostatin Interaction Network* , 2009, The Journal of Biological Chemistry.

[35]  Alexandra Naba,et al.  Towards definition of an ECM parts list: an advance on GO categories. , 2012, Matrix biology : journal of the International Society for Matrix Biology.

[36]  Sylvie Ricard-Blum,et al.  Heparin-protein interactions: from affinity and kinetics to biological roles. Application to an interaction network regulating angiogenesis. , 2014, Matrix biology : journal of the International Society for Matrix Biology.

[37]  Gary D Bader,et al.  PSICQUIC and PSISCORE: accessing and scoring molecular interactions , 2011, Nature Methods.

[38]  Christoph Steinbeck,et al.  The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013 , 2012, Nucleic Acids Res..

[39]  John Parkinson,et al.  Comparative genomics of elastin: Sequence analysis of a highly repetitive protein. , 2007, Matrix biology : journal of the International Society for Matrix Biology.

[40]  Sylvie Ricard-Blum,et al.  Toward a systems level view of the ECM and related proteins: A framework for the systematic definition and analysis of biological systems , 2012, Proteins.

[41]  Gary D. Bader,et al.  Cytoscape App Store , 2013, Bioinform..